NCOR1

nuclear receptor corepressor 1, the group of NCoR/SMRT transcriptional repression complex subunits|Myb/SANT domain containing|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 17:16029064-16218185

Links

ENSG00000141027 ∙ NCBI:9611 ∙ OMIM:600849 ∙ HGNC:7672 ∙ Uniprot:O75376 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NCOR1 gene.

• Inborn genetic diseases (62 variants)
• not provided (26 variants)
• Mitochondrial complex III deficiency nuclear type 2 (5 variants)
• NCOR1-related condition (2 variants)
• NCOR1-related autism spectrum disorder (1 variants)
• Mitochondrial complex III deficiency nuclear type 1 (1 variants)
• Autism;Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCOR1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	11	16
missense			70		4	74
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			3	1	1	5
Total	0	0	73	6	16

Variants in NCOR1

This is a list of pathogenic ClinVar variants found in the NCOR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-16029065-A-G		Mitochondrial complex III deficiency nuclear type 2	Likely benign (Jan 13, 2018)
17-16029084-A-G		Mitochondrial complex III deficiency nuclear type 2	Uncertain significance (Jan 12, 2018)
17-16029111-T-C		Mitochondrial complex III deficiency nuclear type 2	Likely benign (Apr 27, 2017)
17-16029260-T-C		Mitochondrial complex III deficiency nuclear type 2	Uncertain significance (Jan 12, 2018)
17-16029313-T-C		Mitochondrial complex III deficiency nuclear type 2	Benign (Jan 13, 2018)
17-16029408-T-C		Mitochondrial complex III deficiency nuclear type 1	Uncertain significance (Jun 14, 2016)
17-16032417-A-G		not specified	Uncertain significance (Jul 11, 2023)
17-16032453-G-A		not specified	Uncertain significance (Aug 10, 2021)
17-16034796-C-T			Likely benign (Jan 05, 2018)
17-16034826-T-C		NCOR1-related disorder	Benign/Likely benign (Dec 01, 2022)
17-16034860-G-A		not specified	Uncertain significance (Mar 04, 2024)
17-16034873-C-G		not specified	Uncertain significance (Jul 19, 2022)
17-16034943-T-C		not specified	Likely benign (Dec 27, 2023)
17-16039449-G-T		not specified	Uncertain significance (Aug 11, 2022)
17-16039454-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-16039518-C-T		NCOR1-related disorder	Benign/Likely benign (Feb 01, 2024)
17-16039555-T-C		not specified	Uncertain significance (Jul 09, 2021)
17-16039571-C-T		not specified	Uncertain significance (Mar 07, 2023)
17-16039615-G-C		not specified	Uncertain significance (Nov 02, 2021)
17-16039652-A-C		not specified	Uncertain significance (Jan 23, 2024)
17-16040446-G-A		NCOR1-related disorder	Uncertain significance (Mar 30, 2023)
17-16046952-C-T		NCOR1-related disorder	Likely benign (May 06, 2022)
17-16047086-C-T		NCOR1-related disorder	Benign (Apr 01, 2024)
17-16048864-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-16048913-C-T		NCOR1-related disorder	Benign/Likely benign (Oct 28, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCOR1	protein_coding	protein_coding	ENST00000268712	45	189029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.60e-11	125643	0	105	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.94	940	1.35e+3	0.698	0.0000753	15835
Missense in Polyphen		398	668.3	0.59554		7762
Synonymous	0.430	470	482	0.975	0.0000274	4838
Loss of Function	9.44	15	132	0.114	0.00000780	1493

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000358	0.000357
Ashkenazi Jewish	0.00	0.00
East Asian	0.000979	0.000979
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000979	0.000979
South Asian	0.00203	0.00203
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates transcriptional repression by certain nuclear receptors (PubMed:20812024). Part of a complex which promotes histone deacetylation and the formation of repressive chromatin structures which may impede the access of basal transcription factors. Participates in the transcriptional repressor activity produced by BCL6. Recruited by ZBTB7A to the androgen response elements/ARE on target genes, negatively regulates androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). {ECO:0000269|PubMed:14527417, ECO:0000269|PubMed:20812024}.
• Pathway: Thyroid hormone signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Androgen receptor signaling pathway;Adipogenesis;Ovarian Infertility Genes;MECP2 and Associated Rett Syndrome;Pathways Affected in Adenoid Cystic Carcinoma;Notch Signaling Pathway;Developmental Biology;Notch;Disease;Signal Transduction;Gene expression (Transcription);mechanism of gene regulation by peroxisome proliferators via ppara;Circadian Clock;Generic Transcription Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;HDACs deacetylate histones;RNA Polymerase II Transcription;Chromatin modifying enzymes;NR1D1 (REV-ERBA) represses gene expression;Metabolism;Transcriptional regulation of white adipocyte differentiation;Downregulation of SMAD2/3:SMAD4 transcriptional activity;Signaling by NOTCH1;Signaling by NOTCH;AndrogenReceptor;ErbB4 signaling events;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;Chromatin organization;C-MYB transcription factor network;Notch signaling pathway;Nuclear signaling by ERBB4;Signaling by ERBB4;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Signaling by Receptor Tyrosine Kinases;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Notch-mediated HES/HEY network;Diseases of signal transduction;Validated nuclear estrogen receptor alpha network;NOTCH1 Intracellular Domain Regulates Transcription;Signaling events mediated by HDAC Class I;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.625

Intolerance Scores

• loftool: 0.467
• rvis_EVS: -2.14
• rvis_percentile_EVS: 1.5

Haploinsufficiency Scores

• pHI: 0.578
• hipred: Y
• hipred_score: 0.694
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ncor1
• Phenotype: embryo phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: ncor1
• Affected structure: neutrophil
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;transcription by RNA polymerase II;circadian rhythm;regulation of lipid metabolic process;negative regulation of transcription, DNA-templated;negative regulation of JNK cascade;spindle assembly;negative regulation of androgen receptor signaling pathway;regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter;regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter;negative regulation of production of miRNAs involved in gene silencing by miRNA;regulation of fatty acid transport
• Cellular component: histone deacetylase complex;nuclear chromatin;nucleus;nucleoplasm;cytosol;membrane;Sin3 complex;transcriptional repressor complex;mitotic spindle
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II regulatory region DNA binding;RNA polymerase II activating transcription factor binding;chromatin binding;transcription corepressor activity;protein binding;nuclear hormone receptor binding;histone deacetylase binding;sequence-specific DNA binding;transcription regulatory region DNA binding;thyroid hormone receptor binding